Polychlorinated biphenyl (PCB) anaerobic degradation in marine sediments: microcosm study and role of autochthonous microbial communities

Strategy for Remediation of Polychlorinated Biphenyls-Contaminated Soil Through Redox Management Based on Electronegativity of the Contaminants

Literature review reveals that Persistent Organic Pollutants (POPs), such as polychlorinated biphenyls (PCBs), are electron deficient compounds due to the presence of highly electronegative groups. Hence, they are more amenable to anaerobic biodegradation rather than oxidative metabolism. However, the studies on PCBs bioremediation are more inclined towards aerobic treatment. Besides, the past studies are mainly centered on screening and application of PCB-degrading microorganisms. In our opinion the degradative capacity is already present in the native microflora, and choice of electron donor is of paramount importance for faster reductive metabolism of PCBs. In this study, the use of methanol as electron donor with cow dung as the general microbial inoculum resulted in high specific rate of degradation (0.0542-0.0637 /day) for high-chlorinated biphenyls. The % removal of PCBs ranged between 67.7 and 71.7%. It may be the first study on the application of methanol as a cheap electron donor for PCBs biodegradation without bioaugmentation with specifically selected microorganisms.

Sources of polychlorinated biphenyls (PCBs) in sediments of the East China marginal seas: Role of unintentionally-produced PCBs

The production and use of intentionally-produced polychlorinated biphenyls (PCBs) in China have a short history compared with countries of North America and Europe, where technical PCB mixtures were manufactured in large amounts for decades before being banned. Unintentionally-produced PCB emissions increased dramatically in China, leading to unique profiles of PCB burdens. This study first time evaluated 208 individual PCB congeners at 94 sites from surface sediments of the East China Marginal Seas (ECMSs) and explored their sources. Non-technical PCBs transported from atmospheric transport and river discharge played a dominant role in most areas of the ECMSs, while historical residuals of technical PCBs occupied the fine-grained sediments in muddy areas of the central Yellow Sea (YS), regarding to the low sedimentation rate in the central YS. Furthermore, emissions from Taizhou located on the coast of the East China Sea (ECS), which is an important electronic waste dismantling site in East China, contributed additional technical PCBs to the inner shelf of the ECS. Our results indicate that non-technical PCBs have become the dominant PCB species in the ECMSs, and emphasize the synergistic effects of large riverine input, long-range atmospheric transport, and muddy shelf deposition on PCB source and sink of in marginal seas.

Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy)

Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.

mibPOPdb: An online database for microbial biodegradation of persistent organic pollutants

Microbial biodegradation of persistent organic pollutants (POPs) is an attractive, ecofriendly, and cost-efficient clean-up technique for reclaiming POP-contaminated environments. In the last few decades, the number of publications documenting POP-degrading microbes, enzymes, and experimental data sets has continuously increased, necessitating the development of a dedicated web resource that catalogs consolidated information on POP-degrading microbes and tools to facilitate integrative analysis of POP degradation data sets. To address this knowledge gap, we developed the Microbial Biodegradation of Persistent Organic Pollutants Database (mibPOPdb) by accumulating microbial POP degradation information from the public domain and manually curating published scientific literature. Currently, in mibPOPdb, there are 9215 microbial strain entries, including 184 gene (sub)families, 100 enzymes, 48 biodegradation pathways, and 593 intermediate compounds identified in POP-biodegradation processes, and information on 32 toxic compounds listed under the Stockholm Convention environmental treaty. Besides the standard database functionalities, which include data searching, browsing, and retrieval of database entries, we provide a suite of bioinformatics services to facilitate comparative analysis of users' own data sets against mibPOPdb entries. Additionally, we built a Graph Neural Network-based prediction model for the biodegradability classification of chemicals. The predictive model exhibited a good biodegradability classification performance and high prediction accuracy. mibPOPdb is a free data-sharing platform designated to promote research in microbial-based biodegradation of POPs and fills a long-standing gap in environmental protection research. Database URL: http://mibpop.genome-mining.cn/.

Effect of microplastics on microbial dechlorination of a polychlorinated biphenyl mixture (Aroclor 1260)

Microplastics (MPs) and polychlorinated biphenyls (PCBs) generally coexist in the environment, posing risks to public health and the environment. This study investigated the effect of different MPs on the microbial anaerobic reductive dechlorination of Aroclor 1260, a commercial PCB mixture. MP exposure inhibited microbial reductive dechlorination of PCBs, with inhibition rates of 39.43%, 23.97%, and 17.53% by polyethylene (PE), polypropylene (PP), and polystyrene (PS), respectively. The dechlorination rate decreased from 1.63 μM Cl^- d^-1 to 0.99-1.34 μM Cl^- d^-1 after MP amendment. Chlorine removal in the meta-position of PCBs was primarily inhibited by MPs, with no changes in the final PCB dechlorination metabolites. The microbial community compositions in MP biofilms were not significantly different (P > 0.05) from those in suspension culture, although possessing greater Dehalococcoides abundance (0.52-0.81% in MP biofilms; 0.03-0.12% in suspension culture). The co-occurrence network analysis revealed that the presence of MPs attenuated microbial synergistic interactions in the dechlorinating culture systems, which may contribute to the inhibitory effect on microbial PCB dechlorination. These findings are important for comprehensively understanding microbial dechlorination behavior and the environmental fate of PCBs in environments with co-existing PCBs and MPs and for guiding the application of in situ PCB bioremediation.

Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants

Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.

Microbial community structure and metabolic potential in the coastal sediments around the Yellow River Estuary

The Yellow River Estuary and Laizhou Bay are located on the northern Shandong Peninsula in the Bohai Sea in China and have been polluted by intensive anthropogenic activity. However, few studies have focused on the effect of these activities on the microbial communities and their ecological functions in this area. In this study, the combination of 16S rDNA gene sequencing and GeoChip technology was used to analyzed the microbial community component and their functional genes. Thaumarchaeot and Bacteroidetes are the most abundant phyla. The results of correlation analysis and redundancy analysis (RDA) showed water depth (r² = 0.76, P = 0.005), total Na content (r² = 0.63, P = 0.021) and total Ca content (r² = 0.53, P = 0.05) in the sediments were the most significant environmental factors affecting the microbial community. The diversity of the microbial community and signal intensity of functional genes at nearshore sites (N sites) were higher than that at the offshore sites (O sites), but the component of microbial community and functional genes was similar in general. Functional genes for C, N, P and S cycle were detected at both nearshore and offshore sites, which illustrated that microbial communities were active in nutrient cycle. Proteobacteria contributes significantly to material cycle in microbial community. In addition, functional genes related to organic remediation and metal detoxification are also abundant. It indicated that the environmental pollution caused by anthropogenic activities has greatly affected the microbial community components and their biochemical functions in the Yellow River Estuary and surrounding areas. This study reveals the effect of anthropogenic activities on microbial communities and provides the basis for environmental management.

Long-Term Dechlorination of Polychlorinated Biphenyls (PCBs) in Taihu Lake Sediment Microcosms: Identification of New Pathways, PCB-Driven Shifts of Microbial Communities, and Insights into Dechlorination Potential

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) is regarded as an alternative approach for in situ remediation and detoxification in the environment. To better understand the process of PCB dechlorination in freshwater lake sediment, a long-term (108 weeks) dechlorination study was performed in Taihu Lake sediment microcosms with nine parent PCB congeners (PCB5, 12, 64, 71, 105, 114, 149, 153, and 170). Within 108 weeks, the total PCBs declined by 32.8%, while parent PCBs declined by 84.8%. PCB dechlorinators preferred to attack meta- and para-chlorines, principally para-flanked meta and single-flanked para chlorines. A total of 58 dechlorination pathways were observed, and 20 of them were not in 8 processes, suggesting the broad spectrum of PCB dechlorination in the environment. Rare ortho dechlorination was confirmed to target the unflanked ortho chlorine, indicating a potential for complete dechlorination. PCBs drove the shifts of the microbial community structures, and putative dechlorinating bacteria were growth-linked to PCB dechlorination. The distinct jump of RDase genes ardA, rdh12, pcbA4, and pcbA5 was found to be consistent with the commencement of dechlorination. The maintained high level of putative dechlorinating phylum Chloroflexi (including Dehalococcoides and o-17/DF-1), genus Dehalococcoides, and four RDase genes at the end of incubation revealed the long-term dechlorination potential. This work provided insights into dechlorination potential for long-term remediation strategies at PCB-contaminated sites.

Recent advances in PCB removal from historically contaminated environmental matrices

Despite being drastically restricted in the 1970s, polychlorinated biphenyls (PCBs) still belong among the most hazardous contaminants. The chemical stability and dielectric properties of PCBs made them suitable for a number of applications, which then lead to their ubiquitous presence in the environment. PCBs are highly bioaccumulative and persistent, and their teratogenic, carcinogenic, and endocrine-disrupting features have been widely reported in the literature. This review discusses recent advances in different techniques and approaches to remediate historically contaminated matrices, which are one of the most problematic in regard to decontamination feasibility and efficiency. The current knowledge published in the literature shows that PCBs are not sufficiently removed from the environment by natural processes, and thus, the suitability of some approaches (e.g., natural attenuation) is limited. Physicochemical processes are still the most effective; however, their extensive use is constrained by their high cost and often their destructiveness toward the matrices. Despite their limited reliability, biological methods and their application in combinations with other techniques could be promising. The literature reviewed in this paper documents that a combination of techniques differing in their principles should be a future research direction. Other aspects discussed in this work include the incompleteness of some studies. More attention should be given to the evaluation of toxicity during these processes, particularly in terms of monitoring different modes of toxic action. In addition, decomposition mechanisms and products need to be sufficiently clarified before combined, tailor-made approaches can be employed.

Uptake of PCBs into sediment dwellers and trophic transfer in relation to sediment conditions in the Salish Sea

We examined uptake of polychlorinated biphenyls (PCBs) into various marine sediment feeders relative to physical and geochemical factors and transfer to higher trophic levels. PCBs exceeding Canadian Council Ministers of the Environment Guidelines by 6–55× were found in industrialized harbours and some near-outfall sediments, indicating ongoing land input. Sediment PCBs were correlated with organic flux and content. Tissue PCBs were >10× sediment PCBs in all samples and highest in Victoria Harbour infauna, suggesting considerable uptake from these extremely contaminated, organically enriched, chronically disturbed sediments. Sediment PCBs were the primary predictor of tissue lipid PCBs followed by %fines. This results in generally higher tissue PCBs in more depositional regions. The lipid/sediment PCBs (uptake rate) declined with increasing sediment PCBs, acid volatile sulfides and benthos biomass turnover. PCB homologue composition did not change with uptake from sediments or at higher trophic levels, suggesting minimal metabolization in tissues. Trophic bio-magnification occurs since lipid PCBs were 2–100× higher in seal blubber than sediment feeders. PCBs were compared with polybrominated diphenyl ethers (PBDEs) for the same samples. PCBs were highest in industrialized harbours, whereas PBDEs were elevated in harbours but highest near wastewater discharges. This reflects differences in usage history, sediment dynamics, and affinities. PCBs appear to be more bio-accumulative and persistent at higher trophic levels than PBDEs.

Combining sediment management and bioremediation in muddy ports and harbours: A review

This paper reviews two important sources of innovation linked to the maritime environment and more importantly to ports: the potential coupling of sediment management and (bio)remediation. The detrimental effects of dredging are briefly considered, but the focus here is on a sustainable alternative method of managing the problem of siltation. This technique consists of fluidizing the sediment in situ, lowering the shear strength to maintain a navigable under-keel draught. Preliminary investigations show that through this mixing, aeration occurs, which results in a positive remediation effect as well. An overview of port contamination, remediation, and the recent research on aerobic (bio)degradation of port contaminants is made in order to show the potential for such innovative sediment management to reduce dredging need and remediate contaminated mud in ports. This review also highlights the lack of full-scale field applications for such potential remediation techniques, that remain largely confined to the laboratory scale.

Concentrations, sources, and exposure risk of polychlorinated biphenyls in soil profiles of the floodplain of the lower reaches of the River Niger, Nigeria

The concentrations of 28 polychlorinated biphenyls (PCBs) were determined in soils collected at three depths from thirteen different sites along the floodplain of the lower reaches of the River Niger (LRRN) in Nigeria. The aim of the study was to provide data on the levels of contamination, sources of the contaminants, and risks to the ecosystem and humans. Soil samples were Soxhlet extracted with a solvent mixture of dichloromethane (DCM)/n-hexane and cleaned up on a column packed with Florisil and silica gel. The PCBs in the samples were quantified by gas chromatography-mass spectrometry. The Ʃ28 PCB concentrations in the floodplain soils varied between not detected (nd) and 11,151 ng g^-1 for different sampling sites and depths. The PCB concentrations and homologue distribution patterns in soil profiles of the floodplain of the LRRN showed remarkable differences with respect to sites and depths. The results obtained were used to evaluate the ecological and human health risks, which indicated that there is a potential risk to organisms and humans from exposure to PCBs in these soil profiles. The source evaluation as determined by principal component analysis suggested that PCBs in these soil profiles came from burnt circuit boards, cable wires, use of paints, discharges from transformers, long-range migration, and deposition.

Investigating the spatial distribution of polychlorinated biphenyls in sediment in the Pearl River Delta, South China

One hundred forty-three surface sediment (0-5 cm depth) samples were collected from locations representing industrialized areas, less-industrialized areas, and e-waste recycling areas in the Pearl River Delta (PRD). The spatial distribution of polychlorinated biphenyls (PCBs) and their potential adverse effects on aquatic organisms were investigated. The average PCB concentration in the less-industrialized areas (background) in the PRD was approximately 10 ng/g dry weight (dw), which was generally half that found in the industrialized areas (approximately 22 ng/g dw). Severe PCB contamination, with concentrations ranging from 1000 to 26500 ng/g dw, was found in pond sediments collected from e-waste recycling areas. It is very likely that such contamination would have had adverse effects on the aquatic biota there. PCBs in the e-waste recycling areas were dominated by penta- and hex-PCB congeners, which made them significantly different from those found in other regions, where tri- and tetra-PCB congeners were predominant. Higher abundances of less chlorinated congeners were seen in the less-industrialized areas compared to the industrialized areas. Differences in the transport abilities of different congeners, together with dechlorination of higher chlorinated congeners, is the most likely reasons for this.

Anthropogenic influence on the environmental health along Montenegro coast based on the bacterial and chemical characterization

Coastal marine sediments are particularly exposed to human activities. The function of a coastal ecosystem is largely affected by eutrophication, wastewater discharges, chemical pollution, port activities, industry and tourism. Bacterial classification can be used as a measure in assessing the harmful effects on the ecosystem. This study provided insight into the environmental health of the coastal region of Montenegro analyzing the possible impact of PAHs and PCBs upon the bacterial community diversity and function as well as nutrients. Two stations at the shipyards were defined as very high PAH polluted together with PCB concentration exceeding threshold values. The bacterial community at the OTU level clustered together all stations except the most polluted site (SBL), the main tourist destination in Montenegro (BDV) and the estuary site (ADB) forming the independent clusters. Bacterial community based on the OTU level was driven by PAHs, TOC and silt content. The lowest richness and diversity were indicated at the site with the highest concentration of PAHs and PCBs with the highest abundance of Alphaproteobacteria followed by Gammaproteobacteria. OTUs affiliated to phyla BRC1, Dadabacteria and Spirochaetes were present with a total abundance higher than 1% only at the most polluted site indicating their persistence and possible potential for degradation of aromatic compounds. To compare functional capabilities potentially related to biodegradation of aromatic compounds and active transport systems, PICRUSt was used to predict metagenomes of the sediments. From our data, we identified specific bacterial community and predicted metabolic pathways that give us a picture of the environmental health along the coast of Montenegro, which provides us a new insight into human-induced pollution impacts on the coastal ecosystem.

Direct Conversion of Food Waste Extract into Caproate: Metagenomics Assessment of Chain Elongation Process

In a circular economy strategy, waste resources can be used for the biological production of high added-value substances, such as medium chain fatty acids (MCFAs), thus minimising waste and favouring a sustainable process. This study investigates single-stage fermentation processes for the production of MCFAs in a semi-continuous reactor treating the extract of real food waste (FW), without the addition of external electron donors. Two sequential acidogenic fermentation tests were carried out at an organic loading rate (OLR) of 5 and 15 gCOD L⁻¹d⁻¹ with a hydraulic retention time of 4 days and pH controlled at 6 ± 0.2. The highest level of caproate (4.8 g L⁻¹) was observed at OLR of 15 gCOD L⁻¹d⁻¹ with a microbiome mainly composed by lactate-producing Actinomyces, Atopobium, and Olsenella species and caproate-producing Pseudoramibacter. Metagenomic analysis revealed the presence of key enzymes for the production of lactate, such as lactate dehydrogenase and pyruvate ferredoxin oxidoreductase, as well as several enzymes involved in the reverse β-oxidation pathway, thus suggesting the occurrence of a lactate-based chain elongation process.

Bacterial communities as indicators of environmental pollution by POPs in marine sediments

Decades of intensive discharge from industrial activities into coastal systems has resulted in the accumulation of a variety of persistent organic pollutants (POPs) in marine waters and sediments, having detrimental impacts on aquatic ecosystems and the resident biota. POPs are among the most hazardous chemicals originating from industrial activities due to their biotoxicity and resistance to environmental degradation. Bacterial communities are known to break down many of these aromatic compounds, and different members of naturally occurring bacterial consortia have been described to work in syntrophic association to thrive in heavily contaminated waters and sediments, making them potential candidates as bioindicators of environmental pollution. In this study environmental, sampling was combined with chemical analysis of pollutants and high-resolution sequencing of bacterial communities using Next Generation Sequencing molecular biology tools. The aim of the present study was to describe the bacterial communities from marine sediments containing high loads of POPs and to identify relevant members of the resident microbial communities that may act as bioindicators of contamination. Marine sediments were collected from a coastal bay area of the Baltic Sea historically influenced by intense industrial activity, including metal smelting, oil processing, and pulp and paper production. Different types of POPs were detected at high concentrations. Fiberbank sediments, resulting from historic paper industry activity, were found to harbour a clearly distinct bacterial community including a number of bacterial taxa capable of cellulolytic and dechlorination activities. Our findings indicate that specific members of the bacterial communities thrive under increasing levels of POPs in marine sediments, and that the abundances of certain taxa correlate with specific POPs (or groups), which could potentially be employed in monitoring, status assessment and environmental management purposes.

CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) for Complex Environmental Samples

CARD-FISH technique allows us to increase microbial cell detection compared to traditional FISH assays. Specific nonfluorescent oligonucleotide probes targeting 16S rRNA genes are employed and are chemically activated by the binding of tyramide molecules, with the latter able to generate a cascade of fluorescence signals, improving sensitivity and reducing background noise. The technique has been successfully applied for the detection of microorganisms in different environmental matrices and under different growth conditions (including those where cells are characterized by low physiological activity and low ribosome content). This chapter presents a straightforward procedure to execute CARD-FISH analysis, from sample preparation and fixation, to microscopic visualization, along with relevant technical notes.

Spatial characteristics, sources, and ecological and human health risks of polychlorinated biphenyls in sediments from some river systems in the Niger Delta, Nigeria

Polychlorinated biphenyls (PCBs) were quantified in sediments from the lower reaches of the Niger, Ase and Forcados Rivers in Nigeria with the aim of elucidating the sources, spatial characteristics and likely ecological and human health risks relating to exposure to PCBs in the sediments. A total of 28 PCB congeners, including 7 indicator PCBs and 12 dioxin-like PCBs, were identified and quantified after Soxhlet extraction with acetone/n-hexane/dichloromethane by gas chromatography-mass spectrometry. The Σ28 PCB concentrations in sediments from the Niger, Ase and Forcados Rivers ranged from 13.5 to 277 ng g^-1, not detected to 1633 ng g^-1 and 6.9 to 78.6 ng g^-1 respectively. The PCB composition in sediments from these three rivers indicate the dominance of lower chlorinated (2-Cl to 5-Cl) congeners over higher chlorinated (6-Cl to 10-Cl) congeners. The ecological and human health risk assessment suggests potential risks for exposure of both organisms and humans to PCBs in sediments from these three river systems.

Markers of polychlorinated biphenyl (PCB) degradation in highly contaminated soil of Central Russia

The highly polychlorinated biphenyl (PCB)-contaminated historical soil is located in the Serpukhov region (Central Russia). This study evaluates the processes of PCB degradation in the soil under natural conditions. Compositions of industrial mixtures (Sovol, Sovtol, and trichlorodiphenyl) were compared with PCB-contaminated soil from different depths. An increased number of dichlorobiphenyls (6 congeners) were determined in the deeper soil horizons (40-60 cm) in comparison with the surface layer (1 congener). Non-associated with industrial mixture congener, PCB 11 was determined in some soil layers with concentrations reaching 3.6 mg/kg. PCB 11 can be considered as a potential marker of activated degradation processes in highly contaminated soils with industrial mixtures. Aegopodium podagraria reduced total PCB concentrations in the contaminated soil to 25% during pot experiments. Prospective precursors of PCB 11 were significantly depleted (62-88%) after phytoremediation, but this did not increase PCB 11 concentration in the soil.

DPSIR Model Applied to the Remediation of Contaminated Sites. A Case Study: Mar Piccolo of Taranto

The study critically analyses the complex situation of the Mar Piccolo of Taranto (South of Italy), considered one of the most polluted marine ecosystems in Europe. In order to investigate possible cause–effect relationships, useful to plan appropriate planning responses or remediation technologies to be adopted, the Driver–Pressure–State–Impact–Response (DPSIR) model was applied. Methodologically, about 100 references have been considered, whose information was organized according to the logical scheme of the DPSIR. The results showed how the Mar Piccolo is the final receptor of pollutants coming from all industrial and agricultural activities, especially due to its natural hydrogeological network conformation. The anthropic activity represents a critical impact on the ecosystem due to the subsequent marine litter. The mobility of contaminants from sediments to the water column showed the potential risk related to the bioaccumulation of organisms from different trophic levels, posing a threat of unacceptable magnitude to human safety. The paper concludes by discussing the actions currently implemented by the authorities in response to the anthropogenic impacts as well as the need for new ones concerning both plans, programs, and remediation interventions. The case study shows how the DPSIR is a useful framework to organize extensive and heterogeneous information about a complex environmental system, such as the one investigated. This preliminary organization of the available data can represent the starting point for the development of a DPSIR-based Environmental Decision Support System (EDSS) with robust cause–effect relationships.

Structure and diversity of native bacterial communities in soils contaminated with polychlorinated biphenyls

Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) are a group of high-risk synthetic substances for human and environmental health. Currently, the study of sites contaminated by the spillage of equipment PCBs containing have been considered targeted areas for the study of bacterial communities with potential for PCBs degradation. There in isolation of bacterial strains is vital for use in biodegradable processes, such as bacterial bioaugmentation, which accelerates the development of phenomena such as natural attenuation of contaminated sites. The objective of this study was to assess biodiversity of bacteria contained in anthropogenic contaminated soils (H_S and H_P) with PCBs compared to a control sample without contaminant and the modified forest (F) and agricultural (A) soil in the laboratory with 100 mg L⁻¹ PCB. For the analysis of 16S rRNA genes amplified from DNA extracted from the soils evaluated, the latest generation of Illumina Miseq and Sanger sequencing for the cultivable strains were detected. The bacteria identified as the most abundant bacterial phyla for H_S and H_P soil was Proteobacteria (56.7%) and Firmicutes (22.9%), which decreased in F and A soils. The most abundant bacterial genera were Burkholderia, Bacillus, Acinetobacter, Comamonas and Cupriavidus. Several species identified in this study, such as Bacillus cereus, Burkholderia cepacia, Comamonas testosteroni and Acinetobacter pittii have been reported as PCBs degraders. Finally, by means of a principal component analysis (PCA), a correlation between the physical and chemical characteristics of the soils in relation to the relative abundances of the bacteria identified was obtained. The C/N ratio was directly related to the control soil (without contaminant), while SOM maintained a relationship with F and A soils and the bacterial abundances were directly related to Hs and Hp soils due to the presence of aroclor 1260. Bacteria with the ability to tolerate high concentrations of this pollutant are considered for future use in biostimulation and bioaugmentation processes in contaminated soils.

Marine sediment toxicity: A focus on micro- and mesocosms towards remediation

Micro- and/or mesocosms are experimental tools bringing ecologically relevant components of the natural environment under controlled conditions closest to the real world, without losing the advantage of reliable reference conditions and replications, providing a link between laboratory studies and filed studies in natural environments. Here, for the first time, a formal comparison of different types of mesocosm applied to the study of marine contaminants is offered, considering that pollution of coastal areas represented a major concern in the last decades because of the abundance of discharged toxic substances. In particular, the structural characteristics of micro- and mesocosms (m-cosms) used to study marine contaminated sediments were reviewed, focusing on their advantages/disadvantages. Their potentiality to investigate sediment remediation have been discussed, offering new perspective on how the use of m-cosms can be useful for the development of practical application in the development of solutions for contaminated sediment management in the contaminated marine environment.

Priority and emerging micropollutants distribution from coastal to continental slope sediments: A case study of Capbreton Submarine Canyon (North Atlantic Ocean)

Incising continental margins, submarine canyons are key issue for understanding shelf/deep sea exchange of particulate pollutant, impact on marine ecosystem and global geochemical cycling. The occurrence and distribution of 100 priority and emerging micropollutants were investigated in sediments within the first 25 km of the Capbreton submarine area. The most predominant compounds were polycyclic aromatic hydrocarbons (PAHs), trace metals and metalloid (TMs) (e.g. mercury, lead and arsenic), synthetical musks (e.g. musk ketone, galaxolide), UV filters (e.g. octocrylene and 2-ethylhexyl 4-methoxycinnamate, EHMC) as well as some pharmaceuticals (e.g. azithromycin, acetaminophen). Highest concentrations were measured in submarine canyon sediments, distant from the coast and were correlated with both organic carbon and fine fraction contents, where PAHs, EHMC and musk ketone concentrations up to 7116, 32 and 7 ng g^-1 dry weight, respectively. Those results likely demonstrate, that atmospheric inputs of pyrogenic PAHs, and both trapping and transporting of polluted particles along the continuum shore/deep sea by the Capbreton Canyon, might lead to an accumulation of anthropogenic micropollutants. The ecological risk assessment indicates that priority pollutants raise a potentially high risk for benthic organisms (e.g. PAHs, TMs). This might raised a specific concern about how the human can impact this ecosystem.

Anaerobic digestion of mixed urban biowaste: The microbial community shift towards stability

Anaerobic digestion is applied worldwide to treat food waste (FW) with the aim of obtaining renewable bioenergy by exploiting the methane gas produced. However, there are several problems in practical applications, primarily due to system instability. Although exhaustive knowledge regarding anaerobic microbial community composition has been established, few studies have investigated long-term correlations between microbial consortia, operative conditions and feedstock characteristics. Here, microbial community shifts as a response to feedstock variations were investigated in long-term semi-continuous systems, which were evaluated by an in situ cell detection method and 16S rRNA gene amplicon sequencing. FW digestion showed progressive system instability caused by the inhibition of methanogens, which resulted in volatile fatty acid accumulation and process failure at the low organic loading rate (OLR). Conversely, by co-digesting FW with waste-activated sludge (WAS), a stable process with methane yields of up to 0.27 Nm³  kg^-1VS_fed for OLR = 1.7 gVS L^-1d^-1 was achieved. This stabilizing effect was not related to the buffering capacity of WAS, but to its capacity to avoid volatile fatty acid accumulation and falls in pH by overcoming methanogenic activity inhibition. WAS addition promoted the establishment of a stable and active archaeal population in anaerobic co-digestion (AcoD) reactors. The continuous supply of trace elements together with the seeding of microbial functional groups were the main drivers that positively affected process stability.

Identification and characterization of a meta-cleavage product hydrolase involved in biphenyl degradation from Arthrobacter sp. YC-RL1

Polychlorinated biphenyls (PCBs) are a group of persistent organic pollutants (POPs) widely existing in the environment. Arthrobacter sp. YC-RL1 is a biphenyl-degrading bacterium that shows metabolic versatility towards aromatic compounds. A 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate (HOPDA) hydrolase (BphD) gene involved in the biodegradation of biphenyl was cloned from strain YC-RL1 and heterologously expressed in Escherichia coli BL21 (DE3). The recombinant BphD_YC-RL1 was purified and characterized. BphD_YC-RL1 showed the highest activity at 45 °C and pH 7. It was stable under a wide range of temperature (20-50 °C). The enzyme had a K_m value of 0.14 mM, K_cat of 11.61 s^-1, and V_max of 0.027 U/mg. Temperature dependence catalysis exhibited a biphasic Arrhenius Plot with a transition at 20 °C. BphD_YC-RL1 was inactivated by SDS, Tween 20, Tween 80, Trition X-100, DTT, CHAPS, NBS, PMSF, and DEPC, but insensitive to EDTA. Site-directed mutagenesis of the active-site residues revealed that the catalytic triad residues (Ser115, His275, and Asp247) of BphD_YC-RL1 were necessary for its activity. The investigation of BphD_YC-RL1 not only provides new potential enzyme resource for the biodegradation of biphenyl but also helps deepen our understanding on the catalytic process and mechanism.

The effect of redox capacity of humic acids on hexachlorobenzene dechlorination during the anaerobic digestion process

Hexachlorobenzene (HCB) dechlorination affected by humic acids (HA) was evaluated in terms of HA redox capacity, HA concentrations, and microbial community, as well as the correlation between HA redox capacity values and HCB concentrations. With addition of HA in the initial stage, redox capacity values increased by 2.19 meq/L (80 mg/L of HA addition, HA₈₀), 2.51 meq/L (120 mg/L of HA addition, HA₁₂₀), and 3.64 meq/L (200 mg/L of HA addition, HA₂₀₀), respectively. The addition of HA could prominently enhance the HCB degradation rate. However, the concentration and the redox capacity of HA decreased during the anaerobic digestion process. Illumina MiSeq sequencing showed that microbial community affected by HA. Bacillus, Comamonas, and Pseudomonas were the predominant genera during the HCB dechlorination treatment. Moreover, Bacillus and Pseudomonas can improve HA electron transfer capability and promote the dechlorination of HCB.

Microbial diversity assessment of polychlorinated biphenyl-contaminated soils and the biostimulation and bioaugmentation processes

The aim of this study was to know the biodiversity of total microorganisms contained in two polychlorinated biphenyl-contaminated aged soils and evaluate the strategies of bioaugmentation and biostimulation to biodegrade the biphenyls. Besides, the aerobic cultivable microorganisms were isolated and their capacity to biodegrade a commercial mixture of six congeners of biphenyls was evaluated. Biodiversity of contaminated soils was dominated by Actinobacteria (42.79%) and Firmicutes (42.32%) phyla, and others in smaller proportions such as Proteobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes. At the genus level, the majority of the population did not exceed 7% of relative abundance, including Bacillus, Achromobacter, Clostridium, and Pontibacter. Furthermore, four autochthonous bacterial cultures were possible isolates from the soils, which were identified by partial sequencing of the 16S rRNA gene, as Bacillus sp., Achromobacter sp., Pseudomonas stutzeri, and Bacillus subtilis, which were used for the bioaugmentation process. The bioaugmentation and biostimulation strategies achieved a biodegradation of about 60% of both soils after 8 weeks of the process; also, the four isolates were used as mixed culture to biodegrade a commercial mix of six polychlorinated biphenyl congeners; after 4 weeks of incubation, the concentration decreased from 0.5 mg/L to 0.23 mg/L.

Distribution patterns of organic pollutants and microbial processes in marine sediments across a gradient of anthropogenic impact

Marine sediments are part of the hydrological cycle and the ultimate storage compartment of land-derived organic matter, including pollutants. Since relevant microbially-driven processes occurring at benthic level may affect the quality of the overall aquatic system, the necessity for incorporating information about microbial communities functioning for ecosystem modelling is arising. The aim of this field study was to explore the links occurring between sediment contamination patterns by three selected class of organic pollutants (Polycyclic Aromatic Hydrocarbons, PAHs, Nonylphenols, NPs, Bisphenol A, BPA) and major microbial properties (Prokaryotic Biomass, PB; total living biomass, C-ATP; Prokaryotic C Production rate, PCP; Community Respiration rate, CR) across a gradient of anthropogenic pollution. Sediments were sampled from 34 sites selected along 700 km of the western coastline of the Adriatic Sea. Organic contamination was moderate (PAHs <830 ng g^-1; NPs <350  ng g^-1; BPA <38  ng g^-1) and decreased southward. The amount of PAHs-associated carbon (C-PAHs) increased significantly with sediment organic carbon (OC), along with microbial functional rates. The negative relation between PCP/CR ratio and OC indicated the shift toward oxidative processes in response to organic pollution and potential toxicity, estimated as Toxic Equivalents (TEQs). Our outcomes showed that sediment organic contamination and benthic microbial processes can be intimately linked, with potential repercussions on CO₂ emission rates and C-cycling within the detritus-based trophic web.

Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review

Environmental problems such as the deterioration of groundwater quality, soil degradation and various threats to human, animal and ecosystem health are closely related to the presence of high concentrations of organic xenobiotics in the environment. Employing appropriate technologies to remediate contaminated soils is crucial due to the site-specificity of most remediation methods. The limitations of conventional remediation technologies include poor environmental compatibility, high cost of implementation and poor public acceptability. This raises the call to employ biological methods for remediation. Bioremediation and microbe-assisted bioremediation (phytoremediation) offer many ecological and cost-associated benefits. The overall efficiency and performance of bio- and phytoremediation approaches can be enhanced by genetically modified microbes and plants. Moreover, phytoremediation can also be stimulated by suitable plant-microbe partnerships, i.e. plant-endophytic or plant-rhizospheric associations. Synergistic interactions between recombinant bacteria and genetically modified plants can further enhance the restoration of environments impacted by organic pollutants. Nevertheless, releasing genetically modified microbes and plants into the environment does pose potential risks. These can be minimized by adopting environmental biotechnological techniques and guidelines provided by environmental protection agencies and other regulatory frameworks. The current contribution provides a comprehensive overview on enhanced bioremediation and phytoremediation approaches using transgenic plants and microbes. It also sheds light on the mitigation of associated environmental risks.

PCB dechlorination hotspots and reductive dehalogenase genes in sediments from a contaminated wastewater lagoon

Polychlorinated biphenyls (PCBs) are a class of persistent organic pollutants that are distributed worldwide. Although industrial PCB production has stopped, legacy contamination can be traced to several different commercial mixtures (e.g., Aroclors in the USA). Despite their persistence, PCBs are subject to naturally occurring biodegradation processes, although the microbes and enzymes involved are poorly understood. The biodegradation potential of PCB-contaminated sediments in a wastewater lagoon located in Virginia (USA) was studied. Total PCB concentrations in sediments ranged from 6.34 to 12,700 mg/kg. PCB congener profiles in sediment sample were similar to Aroclor 1248; however, PCB congener profiles at several locations showed evidence of dechlorination. The sediment microbial community structure varied among samples but was dominated by Proteobacteria and Firmicutes. The relative abundance of putative dechlorinating Chloroflexi (including Dehalococcoides sp.) was 0.01-0.19% among the sediment samples, with Dehalococcoides sp. representing 0.6-14.8% of this group. Other possible PCB dechlorinators present included the Clostridia and the Geobacteraceae. A PCR survey for potential PCB reductive dehalogenase genes (RDases) yielded 11 sequences related to RDase genes in PCB-respiring Dehalococcoides mccartyi strain CG5 and PCB-dechlorinating D. mccartyi strain CBDB1. This is the first study to retrieve potential PCB RDase genes from unenriched PCB-contaminated sediments.

Advances and perspective in bioremediation of polychlorinated biphenyl-contaminated soils

In recent years, microbial degradation and bioremediation approaches of polychlorinated biphenyls (PCBs) have been studied extensively considering their toxicity, carcinogenicity and persistency potential in the environment. In this direction, different catabolic enzymes have been identified and reported for biodegradation of different PCB congeners along with optimization of biological processes. A genome analysis of PCB-degrading bacteria has led in an improved understanding of their metabolic potential and adaptation to stressful conditions. However, many stones in this area are left unturned. For example, the role and diversity of uncultivable microbes in PCB degradation are still not fully understood. Improved knowledge and understanding on this front will open up new avenues for improved bioremediation technologies which will bring economic, environmental and societal benefits. This article highlights on recent advances in bioremediation of PCBs in soil. It is demonstrated that bioremediation is the most effective and innovative technology which includes biostimulation, bioaugmentation, phytoremediation and rhizoremediation and acts as a model solution for pollution abatement. More recently, transgenic plants and genetically modified microorganisms have proved to be revolutionary in the bioremediation of PCBs. Additionally, other important aspects such as pretreatment using chemical/physical agents for enhanced biodegradation are also addressed. Efforts have been made to identify challenges, research gaps and necessary approaches which in future, can be harnessed for successful use of bioremediation under field conditions. Emphases have been given on the quality/efficiency of bioremediation technology and its related cost which determines its ultimate acceptability.

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination.

High-throughput sequencing revealed novel Dehalococcoidia in dechlorinating microbial enrichments from PCB-contaminated marine sediments

In this study, six PCE-to-ethene dechlorinating cultures, fed with a fermentable substrate (lactate) or hydrogen as electron donor, were obtained from PCB and PCE dechlorinating microcosms constructed with PCB-contaminated marine sediments. A novel Chloroflexi member (OTU-DIS1) affiliated to Dehalococcoidales Incertae Sedis, only distantly related to known dechlorinating bacteria, dominated the enrichment cultures (up to 86% of total OTUs). Sulfate-, thiosulfate- and sulfur-reducing bacteria affiliated to genera Desulfobacter, Dethiosulfatibacter and Desulfuromusa were also found to lesser extent. Remarkably, tceA, vcrA and the bifunctional PCE/PCB dehalogenase genes pcbA1, pcbA4 and pcbA5 were found in all dechlorinating microbial enrichments indicating the coexistence of different Dehalococcoides mccartyi strains. The reductive dechlorination rate in each culture remained unvaried over long-term operation (≈ 30 months) and ranged between 0.85 and 0.97 mmol Cl-1 released L-1 d-1 in the lactate-fed microbial enrichments and between 0.66 and 0.85 mmol Cl-1 released L-1 d-1 in the H2-fed microbial enrichments. Overall, this study highlights the presence of yet unexplored biodiversity in PCBs contaminated marine sediments and indicates these environments as promising sources of novel organohalide-respiring bacteria.

Characterization of polychlorinated biphenyl congeners in surface sediments of the Changjiang Estuary and adjacent shelf by high-resolution sampling and high-resolution mass spectrometry

Due to limited samples and low-resolution analysis, conflicting findings on major polychlorinated biphenyl (PCB) congeners and their origins remain in the East China Sea (ECS). Based on high-resolution sampling and high-resolution mass spectrometry analysis, 72 surface sediment samples from the Changjiang Estuary and adjacent ECS shelf were determined to characterize 39 PCB congeners. PCBs (∑₃₉PCBs) ranged from 0.003 to 16.18ng/g dw, presenting a decreasing seaward trend. Tri-, tetra- and penta-CBs were the main components, accounting for >64% of ∑₃₉PCBs in most samples. Tetra-CBs were the dominant congeners, corresponding to results of sediments from Changjiang middle reach and soils from Changjiang Delta. Comparison between PCBs and sediment properties indicated there may be a deposition boundary of 30°N. In the north, the spatial distribution of PCBs is controlled by Changjiang input and hydrodynamic conditions, while in the south closely related to combination of local source and riverine input.

Identification of two organohalide-respiring Dehalococcoidia associated to different dechlorination activities in PCB-impacted marine sediments

Background

Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) plays a major role in detoxifying anoxic contaminated freshwater and marine sediments from PCBs. Known members of the phylum Chloroflexi are typically responsible for this activity in freshwater sediments, whereas less is known about the microorganisms responsible for this activity in marine sediments. PCB-respiring activities were detected in PCB-impacted marine sediments of the Venice Lagoon. The aim of this work was to identify the indigenous organohalide-respiring microorganisms in such environments and assess their dechlorination specificity against spiked Aroclor™ 1254 PCBs under laboratory conditions resembling the in situ biogeochemistry.

Results

High PCB dechlorination activities (from 150 ± 7 to 380 ± 44 μmol of chlorine removed kg⁻¹ week⁻¹) were detected in three out of six sediments sampled from different locations of the lagoon. An uncultured non-Dehalococcoides phylotype of the class Dehalococcoidia closely related to Dehalobium chlorocoercia DF-1, namely phylotype VLD-1, was detected and enriched up to 10⁹ 16S rRNA gene copies per gram of sediment where dechlorination activities were higher and 25-4/24-4 and 25-2/24-2/4-4 chlorobiphenyls (CB) accumulated as the main tri-/dichlorinated products. Conversely, a different phylotype closely related to the SF1/m-1 clade, namely VLD-2, also enriched highly where lower dechlorination activity and the accumulation of 25-3 CB as main tri-chlorinated product occurred, albeit in the simultaneous presence of VLD-1. Both phylotypes showed growth yields higher or comparable to known organohalide respirers and neither phylotypes enriched in sediment cultures not exhibiting dechlorination.

Conclusions

These findings confirm the presence of different PCB-respiring microorganisms in the indigenous microbial communities of Venice Lagoon sediments and relate two non-Dehalococcoides phylotypes of the class Dehalococcoidia to different PCB dechlorination rates and specificities.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0743-4) contains supplementary material, which is available to authorized users.

Cable Bacteria and the Bioelectrochemical Snorkel: The Natural and Engineered Facets Playing a Role in Hydrocarbons Degradation in Marine Sediments

The composition and metabolic traits of the microbial communities acting in an innovative bioelectrochemical system were here investigated. The system, known as Oil Spill Snorkel, was recently developed to stimulate the oxidative biodegradation of petroleum hydrocarbons in anoxic marine sediments. Next Generation Sequencing was used to describe the microbiome of the bulk sediment and of the biofilm growing attached to the surface of the electrode. The analysis revealed that sulfur cycling primarily drives the microbial metabolic activities occurring in the bioelectrochemical system. In the anoxic zone of the contaminated marine sediment, petroleum hydrocarbon degradation occurred under sulfate-reducing conditions and was lead by different families of Desulfobacterales (46% of total OTUs). Remarkably, the occurrence of filamentous Desulfubulbaceae, known to be capable to vehicle electrons deriving from sulfide oxidation to oxygen serving as a spatially distant electron acceptor, was demonstrated. Differently from the sediment, which was mostly colonized by Deltaproteobacteria, the biofilm at the anode hosted, at high extent, members of Alphaproteobacteria (59%) mostly affiliated to Rhodospirillaceae family (33%) and including several known sulfur- and sulfide-oxidizing genera. Overall, we showed the occurrence in the system of a variety of electroactive microorganisms able to sustain the contaminant biodegradation alone or by means of an external conductive support through the establishment of a bioelectrochemical connection between two spatially separated redox zones and the preservation of an efficient sulfur cycling.

Potential risk reduction of Aroclor 1254 by microbial dechlorination in anaerobic Grasse River sediment microcosms

Aroclor 1254 was the second most produced commercial PCB mixture and is found in soils, sediments and sewage throughout the globe. This commercial PCB mixture is considered particularly toxic because of the relatively high concentrations of congeners with dioxin-like properties. The potential for risk reduction by microbial reductive dechlorination of Aroclor 1254 (A1254) was investigated in sediment microcosms from Grasse River (GR), Massena, NY. The specificity of A1254 dechlorination was doubly- and singly-flanked chlorines in meta positions and to a less extent doubly-flanked para chlorines of 2345-substituted chlorobiphenyl rings. The average dechlorination rate of A1254 was 0.0153 Cl^-/biphenyl/day, and dechlorination rates of single congeners ranged between 0.001 and 0.0074 Cl^-/biphenyl/day. Potential risk associated with A1254 based on the toxic equivalency factors of the dioxin-like congeners was reduced by 83%. Additional potential risk associated with bioaccumulation in fish was reduced by 35% based on biota-sediment accumulation factor estimates for all detected congeners. Finally, the dechlorination end-products were tri- and tetra-chlorobiphenyls with unflanked chlorines, all of which are susceptible to further degradation by aerobic microorganisms. The combined results indicate that microbial reductive dechlorination has the potential for reducing risk associated with toxicity and bioaccumulation in fish in sites contaminated with A1254.

Biodegradation of UV-filters in marine sediments

The degradation of two of the most frequently used UV-filters was investigated through microcosm studies. Marine sediments sampled from two sites in Italy (La Spezia harbour and Sarno river estuary, S1 and S2 respectively) were used to set up aerobic and anaerobic sets of reactors. The sediments were spiked with a methanol solution of 3-(4-methylbenzylidene)camphor (4-MBC) and 2-ethylhexyl 4-(dimethylamino)benzoate (EH-DPAB), at concentrations of either 25 or 50mgkg^-1 each. Methanol (6.3g/L) also served as an organic amendment and growth substrate for improving microbial activity. Monitoring of the biotic and abiotic degradation of the selected contaminants over 16months revealed that 4-MBC biodegradation was very slow and incomplete, whereas over 90% of EH-DPAB was degraded both in the aerobic and the anaerobic reactors by the natural microbial communities of both sediments. Repeated spikes of EH-DPAB were followed by complete decay, characterised by first-order kinetics. The calculated kinetic rate constants under aerobic and anaerobic conditions were similar. In reactors inoculated with the S1 sediment the degradation rate constants progressively increased after each spike, up to the value of 0.039d^-1. For the S2 sediment the rate constant was around 0.020d^-1 throughout the duration of the experiment. Mass spectrometry analysis of sediment extracts allowed detection of potential transformation products of EH-DPAB and 4-MBC. Moreover, the natural microbial community of the sediments was studied using the CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) both in the initial sediments and after degradation under aerobic and anaerobic conditions.

Microbial-Catalyzed Reductive Dechlorination of Polychlorinated Biphenyls in Hudson and Grasse River Sediment Microcosms: Determination of Dechlorination Preferences and Identification of Rare Ortho Removal Pathways

Biodegradation of polychlorinated biphenyls (PCBs) is an important transformation and detoxification route in the environment. To better understand the influence of PCB congener compositions on dechlorination, sediments from two rivers, Hudson and Grasse, and two PCB mixtures (PCB 5/12, 64/71, 105/114, and 149/153/170 in Mixture 1 and PCB 5/12, 64/71, 82/97/99, and 144/170 in Mixture 2) were used for this microcosm study. The Grasse River sediment microcosms exhibited more extensive dechlorination than the Hudson River sediment microcosms. The extent of dechlorination was predominantly controlled by sediment itself, not by the PCB compositions. Rare ortho dechlorination, targeting mono-ortho PCB congeners was observed in Grasse sediment, indicating a potential for full dechlorination of some PCBs in this sediment. The identified ortho dechlorination pathways were PCB 28 (24-4-CB) to PCB 15 (4-4-CB) and PCB 25 (24-3-CB) to PCB 13(3-4-CB). The relative abundances of Dehalococcoides were much higher in both sediments spiked with PCBs. An apparent increase of Dehalococcoides 16S rRNA genes coincided with the commencement of dechlorination. The dechlorination preferences were identified using a modified data analysis approach focusing on chlorine neighboring conditions. In both sediments, the overall dechlorination preferred meta > para > ortho. Specially, ortho-/double-flanked meta-chlorines were primarily targeted followed by single-/double-flanked para-chlorines.

First evidence on the occurrence and dynamics of Dehalococcoides mccartyi PCB-dechlorinase genes in marine sediment during Aroclor1254 reductive dechlorination

The present study evaluates the PCB-dehalorespiring capabilities and dynamics of indigenous Dehalococcoides mccartyi population in a PCB contaminated marine sediment. Specialized PCB-dechlorinase genes pcbA1, pcbA4 and pcbA5 previously characterized in pure cultures of D. mccartyi, were here found for the first time in environmental samples. Reductive dechlorination was stimulated by spiking Aroclor1254 to the sediment and by imposing strictly anaerobic conditions both with and without bioaugmentation with a Dehalococcoides mccartyi enrichment culture. In line with the contaminant dechlorination kinetics, Dehalococcoides population increased during the entire incubation period showing growth yields of 4.94E+07 Dehalococcoides per μmolCl^-1 and 7.30E+05 Dehalococcoides per μmolCl^-1 in the marine sediment with and without bioaugmentation respectively. The pcbA4 and pcbA5 dechlorinase genes, and to a lesser extent pcbA1 gene, were enriched during the anaerobic incubation suggesting their role in Aroclor1254 dechlorination under salinity conditions.

Plant-assisted bioremediation of a historically PCB and heavy metal-contaminated area in Southern Italy

A plant-assisted bioremediation strategy was applied in an area located in Southern Italy, close to the city of Taranto, historically contaminated by polychlorinated biphenyls (PCBs) and heavy metals. A specific poplar clone (Monviso) was selected for its ability to promote organic pollutant degradation in the rhizosphere, as demonstrated elsewhere. Chemical and microbiological analyses were performed at the time of poplar planting in selected plots at different distances from the trunk (0.25-1m) and at different soil depths (0-20 and 20-40cm), at day 420. A significant decrease in PCB congeners and a reduction in all heavy metals was observed where the poplar trees were present. No evidence of PCB and heavy metal reduction was observed in the non poplar-vegetated soil. Microbial analyses (dehydrogenase activity, cell viability, microbial abundance) of the autochthonous microbial community showed an improvement in soil quality. In particular, microbial activity generally increased in the poplar-rhizosphere and a positive effect was observed in some cases at up to 1m distance from the trunk and up to 40cm depth. The Monviso clone was effective in promoting both a general decrease in contaminant occurrence and an increase in microbial activity in the chronically polluted area a little more than one year after planting.

Microbiome Dynamics of a Polychlorobiphenyl (PCB) Historically Contaminated Marine Sediment under Conditions Promoting Reductive Dechlorination

The toxicity of polychlorinated biphenyls (PCB) can be efficiently reduced in contaminated marine sediments through the reductive dechlorination (RD) process lead by anaerobic organohalide bacteria. Although the process has been extensively investigated on PCB-spiked sediments, the knowledge on the identity and metabolic potential of PCB-dechlorinating microorganisms in real contaminated matrix is still limited. Aim of this study was to explore the composition and the dynamics of the microbial communities of the marine sediment collected from one of the largest Sites of National Interest (SIN) in Italy (Mar Piccolo, Taranto) under conditions promoting the PCBs RD. A long-term microcosm study revealed that autochthonous bacteria were able to sustain the PCB dechlorination at a high extent and the successive addition of an external fermentable organic substrate (lactate) caused the further depletion of the high-chlorinated PCBs (up to 70%). Next Generation Sequencing was used to describe the core microbiome of the marine sediment and to follow the changes caused by the treatments. OTUs affiliated to sulfur-oxidizing ε-proteobacteria, Sulfurovum, and Sulfurimonas, were predominant in the original sediment and increased up to 60% of total OTUs after lactate addition. Other OTUs detected in the sediment were affiliated to sulfate reducing (δ-proteobacteria) and to organohalide respiring bacteria within Chloroflexi phylum mainly belonging to Dehalococcoidia class. Among others, Dehalococcoides mccartyi was enriched during the treatments even though the screening of the specific reductive dehalogenase genes revealed the occurrence of undescribed strains, which deserve further investigations. Overall, this study highlighted the potential of members of Dehalococcoidia class in reducing the contamination level of the marine sediment from Mar Piccolo with relevant implications on the selection of sustainable bioremediation strategies to clean-up the site.

Benthic ecosystem functioning in the severely contaminated Mar Piccolo of Taranto (Ionian Sea, Italy): focus on heterotrophic pathways

The benthic ecosystem functioning is a rarely applied holistic approach that integrates the main chemical and biological features of the benthic domain with the key processes responsible for the flux of energy and C through the system. For the first time, such conceptual model, with an emphasis on the heterotrophic pathways, has been applied to the sediments at four stations within one of the most polluted coastal areas in Italy: the Mar Piccolo of Taranto. The functioning of the benthic ecosystem was different according to the investigated site. Nearby the military arsenal, i.e., the main source of organic contaminants and heavy metals, the system seemed inhibited at all the investigated structural and functional levels. Slow microbial processes of C reworking together with very limited densities of benthic fauna suggested a modest transfer of C both into a solid microbial loop and to the higher trophic levels. On the other hand, the ingression of marine water through the "Navigabile" channel seemed to stimulate the organic matter degradation and, consequently, the proliferation of meiofauna and macrofauna. In the innermost part of the basin, the system functioning, to some extent, is less impacted by contaminants and more influenced by mussel farms. The organic matter produced by these bivalves fueled faster C reworking by benthic prokaryotes and enhanced the proliferation of filter feeders.

PCBs attenuation and abundance of Dehalococcoides spp., bphC, CheA, and flic genes in typical polychlorinated biphenyl-polluted soil under floody and dry soil conditions

This study investigates PCBs attenuation and the abundance of active polychlorinated-degrading Dehalococcoides spp. biphenyl dioxygenase (bphC), chemotaxis (CheA), and flagellum (flic) genes in floody and dry soil conditions polluted with polychlorinated biphenyls. The results revealed that total PCBs, high chlorinated PCBs (>4 cl), and less chlorinated PCBs (<4 cl) decreased with the passage of time in floody and dry soil conditions. The reduction of total PCBs (13.87%) and less chlorinated PCBs (15.39%) was more in dry soil than floody soil, while high chlorinated PCBs showed more reduction in floody soil (8.06%) than dry soil. Dehaloccoides spp., bphC, CheA, and flic genes indicated temporal dynamics in abundance in floody and dry soil conditions. The highest abundance was 1.6 × 10(9), 3.7 × 10(4), and 3.6 × 10(2) copies in floody and 1.6 × 10(4) copies in dry soil for Dehalococcoides spp., bphC, CheA, and flic, respectively. Multivariate statistics (RDA) revealed that Dehaloccoides spp. were positively influenced by the higher chlorinated PCBs and soil physical properties, CheA gene with floody soil, flic gene with total PCBs and less chlorinated PCBs, and bphC gene was affected with moisture contents and less chlorinated PCBs. This study provides new insight in the attenuation of PCBs and the abundance of active Dehalococcoides spp. and genes in PCBs polluted soil under floody and dry soil conditions.

Patterns of benthic bacterial diversity in coastal areas contaminated by heavy metals, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs)

Prokaryotes in coastal sediments are fundamental players in the ecosystem functioning and regulate processes relevant in the global biogeochemical cycles. Nevertheless, knowledge on benthic microbial diversity patterns across spatial scales, or as function to anthropogenic influence, is still limited. We investigated the microbial diversity in two of the most chemically polluted sites along the coast of Italy. One site is the Po River Prodelta (Northern Adriatic Sea), which receives contaminant discharge from one of the largest rivers in Europe. The other site, the Mar Piccolo of Taranto (Ionian Sea), is a chronically polluted area due to steel production plants, oil refineries, and intense maritime traffic. We collected sediments from 30 stations along gradients of contamination, and studied prokaryotic diversity using Illumina sequencing of amplicons of a 16S rDNA gene fragment. The main sediment variables and the concentration of eleven metals, polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) were measured. Chemical analyses confirmed the high contamination in both sites, with concentrations of PCBs particularly high and often exceeding the sediment guidelines. The analysis of more than 3 millions 16S rDNA sequences showed that richness decreased with higher contamination levels. Multivariate analyses showed that contaminants significantly shaped community composition. Assemblages differed significantly between the two sites, but showed wide within-site variations related with spatial gradients in the chemical contamination, and the presence of a core set of OTUs shared by the two geographically distant sites. A larger importance of PCB-degrading taxa was observed in the Mar Piccolo, suggesting their potential selection in this historically polluted site. Our results indicate that sediment contamination by multiple contaminants significantly alter benthic prokaryotic diversity in coastal areas, and suggests considering the potential contribution of the resident microbes to contaminant bioremediation actions.